(New) BAM Analysis kit 1.6 - released with significant upgrades and improvements (more ...)

Monday, June 29, 2015

Ancient DNA of Black Death Victim #8291

Ancient DNA was sequenced from tooth of sample #8291, a Black Death victim from c. 1348 AD, East Smithfield Cemetery, London, UK. I converted the raw data of these samples into formats familiar to genetic genealogists. The complete SNPs are available for download. However, there is not much common SNPs when filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry, hence not uploaded to GEDmatch. Haplogroups, site location, and age of the sample etc as per the authors can be found in Ancient DNA page.

Download: 
Reference:
Schuenemann, Verena J., et al. "Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death." Proceedings of the National Academy of Sciences 108.38 (2011): E746-E752.

Data Used

Tuesday, June 23, 2015

Two Ancient DNA from indigenous Botocudos of Brazil

Understanding the peopling of the Americas remains an important and challenging question. The authors present 14C dates, and morphological, isotopic and genomic sequence data from two human skulls from the state of Minas Gerais, Brazil, part of one of the indigenous groups known as ‘Botocudos’. I converted the raw data of these samples into formats familiar to genetic genealogists. The complete SNPs are available for download. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry and uploaded to GEDmatch. Haplogroups, site location, GEDmatch ID and age of the sample etc as per the authors can be found in Ancient DNA page.

Download: 
Reference:
Malaspinas, Anna-Sapfo, Oscar Lao, Hannes Schroeder, Morten Rasmussen, Maanasa Raghavan, Ida Moltke, Paula F. Campos et al. "Two ancient human genomes reveal Polynesian ancestry among the indigenous Botocudos of Brazil." Current Biology 24, no. 21 (2014): R1035-R1037.

Data Used

Ancient DNA from 10 Petrous Bones

The authors carried out intra-petrous comparisons for 10 petrous bones from specimens from Holocene archaeological contexts across Eurasia dated between 10,000-1,800 calibrated years before present (cal. BP). The methodology they used may potentially enable ancient DNA analyses of samples from hot regions that are otherwise not amenable to ancient DNA analyses. The ancient DNA from 10 petrous bones were provided by authors with their paper. I converted the raw data of these samples into formats familiar to genetic genealogists. The complete SNPs are available for download. I also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry but found significantly less common SNPs. Haplogroups, site location, age of the sample etc as per the authors can be found in Ancient DNA page.

Download: 
Reference:
Ron Pinhasi , Daniel Fernandes, Kendra Sirak, Mario Novak, Sarah Connell, Songül Alpaslan-Roodenberg, Fokke Gerritsen, Vyacheslav Moiseyev, Andrey Gromov, Pál Raczky, Alexandra Anders, Michael Pietrusewsky, Gary Rollefson, Marija Jovanovic, Hiep Trinhhoang, Guy Bar-Oz, Marc Oxenham, Hirofumi Matsumura, Michael Hofreiter et al. "Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone" doi:10.1371/journal.pone.0129102

Data Used

Saturday, June 13, 2015

101 Ancient Eurasian DNA

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Authors had provided 101 ancient genomes with their publications. Alex of Russian forum.molgen.org community, Sergey (ethnocalc (at) mail.ru) and myself converted the raw data of these sample into formats familiar to genetic genealogists. The complete SNPs are available for download. We also filtered with SNPs tested by DNA testing companies like FTDNA, 23andMe and Ancestry. If we find it to have more SNPs common with them, we uploaded to GEDMatch and the reference GEDmatch IDs Haplogroups, site location, age of the sample etc as per the authors can be found in Ancient DNA page.

Download: 
Reference:
Morten E. Allentoft, Martin Sikora, Karl-Göran Sjögren, Simon Rasmussen, Morten Rasmussen, Jesper Stenderup, Peter B. Damgaard, Hannes Schroeder, Torbjörn Ahlström, Lasse Vinner, Anna-Sapfo Malaspinas, Ashot Margaryan, Tom Higham, David Chivall, Niels Lynnerup, Lise Harvig, Justyna Baron, Philippe Della Casa, Paweł Dąbrowski, Paul R. Duffy, Alexander V. Ebel, Andrey Epimakhov, Karin Frei, Mirosław Furmanek, Tomasz Gralak et al. "Population genomics of Bronze Age Eurasia" doi:10.1038/nature14507

Data Used

Sunday, February 15, 2015

Health Variant Report


The tool is not intended to provide any health interpretations. If you notice the result requires health attention then please visit a physician and do proper tests and confirm.


Variant Report takes the risk information from a configurable file 'app.conf' and generates report with health related information from autosomal files. Currently, 23andMe, FTDNA and Ancestry files are supported.

Prerequisites: Microsoft .Net Framework 4.0

Usage: Edit the app.conf in a notepad (or any text editor), add the required risk alleles and generate the report. The app.conf is a comma separated file with the following fields. Category, Gene, RSID, Risk Allele, Notes and any line starting with # is a comment.

Screenshot:





Download : Variant Report.zip (111 KB)

Source Code at GitHub.

Change Log
Version 1.0
  • Initial Release.